comparison ggplot2_pca.xml @ 5:fcb6a19960c6 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"

4:7e616a1bdb07

<tool id="ggplot2_pca" name="PCA plot w ggplot2" version="@VERSION@">
    <expand macro="bio_tools"/>
    <macros>
        <import>macros.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="0.4.3">r-ggfortify</requirement>
        <requirement type="package" version="1.2.1">r-svglite</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
cat '$script' &&
Rscript '$script'
    ]]></command>

            </when>
            <when value="define_groups">
                <repeat name="group_names" min="2" title="Group" help="Select the samples for this group">
                    <param name="groupName" type="text" optional="false" label="Group name"
                        help="Use short names, avoid special characters and numbers at the beginning of the name (The names might be changed by the program to make them conform to processing in R)">
                        <validator type="no_options" message="Please choose a name for this group!"/>
                    </param>
                    <param name="groupCols" type="data_column" data_ref="input1" multiple="true" min="1" label="Columns for group"
                        help="WARNING: please use columns indices after removing the row name column if selected in second section!">
                        <validator type="no_options" message="Select at least one column for each group!"/>
                        <!--<filter type="remove_value" meta_ref="groupCols" />-->
                    </param>
                    <conditional name="color_cond">
                        <param name="color_bool" type="select" label="Change colors">
                            <option value="default" selected="true">Default ggplot colors</option>

5:fcb6a19960c6

<tool id="ggplot2_pca" name="PCA plot w ggplot2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
    <expand macro="bio_tools"/>
    <macros>
        <import>macros.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="0.4.13">r-ggfortify</requirement>
        <requirement type="package" version="2.0.0">r-svglite</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
cat '$script' &&
Rscript '$script'
    ]]></command>

            </when>
            <when value="define_groups">
                <repeat name="group_names" min="2" title="Group" help="Select the samples for this group">
                    <param name="groupName" type="text" optional="false" label="Group name"
                        help="Use short names, avoid special characters and numbers at the beginning of the name (The names might be changed by the program to make them conform to processing in R)">
                        <sanitizer invalid_char="">
                            <valid initial="string.letters,string.digits">
                                <add value=":" />
                                <add value="-" />
                                <add value=" " />
                                <add value="_" />
                            </valid>
                        </sanitizer>
                        <validator type="regex" message="Value may include alphanumeric characters, colons, dashes, underscores and spaces.">[0-9a-zA-Z:-_ ]+</validator>
                    </param>
                    <param name="groupCols" type="data_column" data_ref="input1" multiple="true" min="1" label="Columns for group"
                        help="WARNING: please use columns indices after removing the row name column if selected in second section!">
                        <validator type="regex" message="Select at least one column for each group!">[0-9a-zA-Z:-_ ]+</validator>
                        <!--<filter type="remove_value" meta_ref="groupCols" />-->
                    </param>
                    <conditional name="color_cond">
                        <param name="color_bool" type="select" label="Change colors">
                            <option value="default" selected="true">Default ggplot colors</option>